diff options
Diffstat (limited to 'notes/bootstrap')
| -rw-r--r-- | notes/bootstrap/import_timing_20190129.txt | 10 | ||||
| -rw-r--r-- | notes/bootstrap/import_timing_20190130.txt | 228 |
2 files changed, 237 insertions, 1 deletions
diff --git a/notes/bootstrap/import_timing_20190129.txt b/notes/bootstrap/import_timing_20190129.txt index 6d635f92..30b7bdbf 100644 --- a/notes/bootstrap/import_timing_20190129.txt +++ b/notes/bootstrap/import_timing_20190129.txt @@ -6,6 +6,8 @@ Made a number of changes since yesterday's import, so won't be surprised if run in to problems. Plan is to make any fixes and push through to the end to turn up any additional issues/bugs, then iterate yet again if needed. +NOTE: this import ended up being abandoned (too slow) in lieu of 2019-01-30. + ## Service up/down sudo service fatcat-web stop @@ -108,6 +110,14 @@ up any additional issues/bugs, then iterate yet again if needed. would take... about an hour to restart, might save 20+ hours, might waste 14? + Counter({'total': 5005785, 'insert': 4319312, 'exists': 457819, 'skip': 228654, 'update': 0}) + 531544.60user 13597.32system 60:38:43elapsed 249%CPU (0avgtext+0avgdata 448748maxresident)k + 124037840inputs+395235552outputs (140major+41973732minor)pagefaults 0swaps + + real 3638m43.712s => 60 hours (!!!) + user 8944m37.944s + sys 232m25.200s + export FATCAT_AUTH_SANDCRAWLER="..." export FATCAT_API_AUTH_TOKEN=$FATCAT_AUTH_SANDCRAWLER time zcat /srv/fatcat/datasets/ia_papers_manifest_2018-01-25.matched.json.gz | pv -l | time parallel -j12 --round-robin --pipe ./fatcat_import.py --batch-size 50 matched --bezerk-mode - diff --git a/notes/bootstrap/import_timing_20190130.txt b/notes/bootstrap/import_timing_20190130.txt index d102e39f..92f98163 100644 --- a/notes/bootstrap/import_timing_20190130.txt +++ b/notes/bootstrap/import_timing_20190130.txt @@ -2,6 +2,8 @@ The QA import is running really slow; this is a parallel attempt in case things are faster on the fatcat-prod2-vm machine, with 50 batch size and bezerk mode. +NOTE: this ended up being the successful/"final" bootstrap import. + ## Service up/down sudo service fatcat-web stop @@ -109,10 +111,234 @@ are faster on the fatcat-prod2-vm machine, with 50 batch size and bezerk mode. time zcat /srv/fatcat/datasets/2018-09-23-0405.30-dumpgrobidmetainsertable.longtail_join.filtered.tsv.gz | pv -l | time parallel -j12 --round-robin --pipe ./fatcat_import.py --batch-size 50 grobid-metadata - --longtail-oa -## Bugs encountered + 1.6M 2:02:05 [ 218 /s] + Counter({'total': 133095, 'insert': 120176, 'inserted.release': 120176, 'exists': 12919, 'skip': 0, 'update': 0}) + 20854.82user 422.09system 2:02:12elapsed 290%CPU (0avgtext+0avgdata 63816maxresident)k + 29688inputs+21057912outputs (118major+809972minor)pagefaults 0swaps + + real 122m12.533s + user 350m14.824s + sys 7m29.820s + +## After Import Stats + + bnewbold@wbgrp-svc503$ df -h . + Filesystem Size Used Avail Use% Mounted on + /dev/vda1 1.8T 591G 1.1T 36% / + + Size: 294.82G + + select count(*) from changelog => 2,306,900 + + + table_name | table_size | indexes_size | total_size +--------------------------------------------------------------+------------+--------------+------------ + "public"."refs_blob" | 70 GB | 1896 MB | 72 GB + "public"."release_rev" | 36 GB | 32 GB | 68 GB + "public"."release_contrib" | 25 GB | 23 GB | 48 GB + "public"."release_edit" | 9342 MB | 10 GB | 19 GB + "public"."work_edit" | 9342 MB | 10 GB | 19 GB + "public"."release_ident" | 6334 MB | 10235 MB | 16 GB + "public"."work_ident" | 6333 MB | 10235 MB | 16 GB + "public"."file_rev_url" | 6085 MB | 2251 MB | 8337 MB + "public"."work_rev" | 4092 MB | 3795 MB | 7887 MB + "public"."file_rev" | 1706 MB | 2883 MB | 4589 MB + "public"."abstracts" | 4089 MB | 300 MB | 4390 MB + "public"."file_edit" | 1403 MB | 1560 MB | 2963 MB + "public"."file_ident" | 944 MB | 1529 MB | 2473 MB + "public"."file_rev_release" | 889 MB | 1558 MB | 2447 MB + "public"."release_rev_abstract" | 404 MB | 536 MB | 941 MB + "public"."creator_rev" | 371 MB | 457 MB | 827 MB + "public"."creator_edit" | 377 MB | 420 MB | 797 MB + "public"."editgroup" | 480 MB | 285 MB | 766 MB + "public"."creator_ident" | 255 MB | 412 MB | 667 MB + "public"."changelog" | 135 MB | 139 MB | 274 MB + "public"."container_rev" | 31 MB | 11 MB | 42 MB + "public"."container_edit" | 10 MB | 12 MB | 22 MB + "public"."container_ident" | 7216 kB | 12 MB | 19 MB + + relname | too_much_seq | case | rel_size | seq_scan | idx_scan +----------------------+--------------+------+-------------+----------+----------- + creator_edit | -94655 | OK | 395558912 | 2 | 94657 + container_edit | -94655 | OK | 10911744 | 2 | 94657 + file_edit | -94655 | OK | 1470627840 | 2 | 94657 + work_edit | -94655 | OK | 9793445888 | 2 | 94657 + release_edit | -94655 | OK | 9793241088 | 2 | 94657 + container_rev | -1168077 | OK | 32546816 | 3 | 1168080 + file_rev_release | -3405015 | OK | 931627008 | 2 | 3405017 + file_rev_url | -3405015 | OK | 6379298816 | 2 | 3405017 + changelog | -3883131 | OK | 141934592 | 382 | 3883513 + abstracts | -8367919 | OK | 4011868160 | 1 | 8367920 + creator_ident | -9066121 | OK | 267124736 | 5 | 9066126 + creator_rev | -14129509 | OK | 388431872 | 3 | 14129512 + release_contrib | -17121962 | OK | 26559053824 | 3 | 17121965 + release_rev_abstract | -17123930 | OK | 423878656 | 3 | 17123933 + file_ident | -18428366 | OK | 989888512 | 5 | 18428371 + refs_blob | -50251199 | OK | 15969484800 | 1 | 50251200 + container_ident | -74332007 | OK | 7364608 | 5 | 74332012 + file_rev | -99555196 | OK | 1788166144 | 4 | 99555200 + release_ident | -132347345 | OK | 6639624192 | 5 | 132347350 + work_rev | -193625747 | OK | 4289314816 | 1 | 193625748 + work_ident | -196604815 | OK | 6639476736 | 5 | 196604820 + editgroup | -214491911 | OK | 503414784 | 3 | 214491914 + release_rev | -482813156 | OK | 38609838080 | 11 | 482813167 +(23 rows) + +## Dump Stats / Process + + DATABASE_URL=fatcat_prod ./ident_table_snapshot.sh /tmp + + postgres@wbgrp-svc503:/srv/fatcat/src/extra/sql_dumps$ DATABASE_URL=fatcat_prod ./ident_table_snapshot.sh /tmp + Will move output to '/tmp' + Running SQL (from 'fatcat_prod')... + BEGIN + COPY 1 + COPY 3906704 -> creators + COPY 107826 -> containers + COPY 14378465 -> files + COPY 3 -> filesets + COPY 3 -> webcaptures + COPY 96812903 -> releases + COPY 96812903 -> works + COPY 2306900 -> changelog + ROLLBACK + + Done: /tmp/fatcat_idents.2019-02-01.214959.r2306900.tar.gz + + fatcat-export: + x files + x containers + - releases_extended (TODO: estimate time to dump based on file timestamps) + + cat /tmp/fatcat_ident_releases.tsv | ./target/release/fatcat-export release --expand files,filesets,webcaptures,container -j8 | pv -l | gzip > /srv/fatcat/snapshots/release_export_expanded.json.gz + + 96.8M 7:37:51 [3.52k/s] + + -rw-rw-r-- 1 webcrawl webcrawl 64G Feb 2 05:45 release_export_expanded.json.gz + + sql dumps: + + time sudo -u postgres pg_dump --verbose --format=tar fatcat_prod | pigz > /srv/fatcat/snapshots/fatcat_private_dbdump_${DATESLUG}.tar.gz + + real 112m34.310s + user 296m46.112s + sys 22m35.004s + + -rw-rw-r-- 1 bnewbold bnewbold 81G Feb 2 04:15 fatcat_private_dbdump_2019-02-02.022209.tar.gz + +Looking for repeated SHA-1 and DOI: + + zcat file_hashes.tsv.gz | cut -f 3 | sort -S 8G | uniq -cd | sort -n > repeated_sha1.tsv + => none + + zcat release_extid.tsv.gz | cut -f 3 | sort -S 8G | uniq -cd | sort -n > repeated_doi.tsv + => a few million repeated *blank* lines... could filter out? + +## Load Stats / Progress + export LC_ALL=C.UTF-8 + time zcat /srv/fatcat/snapshots/release_export_expanded.json.gz | pv -l | ./fatcat_export.py transform-releases - - | esbulk -verbose -size 20000 -id ident -w 8 -index fatcat_release -type release + time zcat /srv/fatcat/snapshots/container_export.json.gz | pv -l | ./fatcat_export.py transform-containers - - | esbulk -verbose -size 20000 -id ident -w 8 -index fatcat_container -type container + + + time zcat /srv/fatcat/snapshots/2019-01-30/container_export.json.gz | pv -l | ./fatcat_export.py transform-containers - - | esbulk -verbose -size 20000 -id ident -w 8 -index fatcat_container -type container + + real 0m58.528s + user 1m0.396s + sys 0m2.412s + + # very python-CPU-limited, so crank that -j20 + # hadn't used '--linebuffer' with parallel before, but otherwise it holds + # on to all the output lines before passing on to the next pipe program + time zcat /srv/fatcat/snapshots/2019-01-30/release_export_expanded.json.gz | pv -l | parallel -j20 --linebuffer --round-robin --pipe ./fatcat_export.py transform-releases - - | esbulk -verbose -size 20000 -id ident -w 8 -index fatcat_release -type release + + 165k 0:00:10 [18.4k/s] + + 2019/02/02 09:30:49 96812900 docs in 2h27m32.835681602s at 10935.807 docs/s with 8 workers + 2019/02/02 09:30:49 applied setting: {"index": {"refresh_interval": "1s"}} with status 200 OK + 2019/02/02 09:30:49 applied setting: {"index": {"number_of_replicas": "1"}} with status 200 OK + 2019/02/02 09:31:03 index flushed: 200 OK + + real 147m46.387s + user 2621m40.420s + sys 56m11.456s + + sudo su postgres + dropdb fatcat_prod + #zcat fatcat_private_dbdump_2019-02-02.022209.tar.gz | pg_restore --clean --if-exists --create --exit-on-error -d fatcat_prod + createdb fatcat_prod + time zcat fatcat_private_dbdump_2019-02-02.022209.tar.gz | pg_restore --exit-on-error --clean --if-exists --dbname fatcat_prod + + seems to go pretty fast, so multiple jobs probably not needed + + real 284m40.448s + user 58m45.240s + sys 7m33.600s + +DONE: delete old elastic index + +## Bugs/Issues encountered + +x in_ia_sim is broken; not passing through +x elastic port (9200) was not open to cluster + => but should close; should be over HTTP +x elasticsearch host wrong (should be search.fatcat.wiki) + => search.fatcat.wiki +x postgres config wasn't actually getting installed in the right place by + ansible (!!!), which probably had crazy effects on performance, etc +x postgres version confusion was because both versions (server and client) can + be installed in parallel, and older version "wins". wiping VM would solve this. +x should try pigz for things like ident_table_snapshot and exports? these seem to be gzip-limited +- fatcat-export and pg_dump seem to mutually lock (transaction-wise), which is + unexpected. fatcat-export should have very loose (low-priority) transaction + scope, because it already has the full release_rev id, and pg_dump should + also be in background/non-linear mode (except for "public" dumps?) + => this was somewhat subtle; didn't completely lock +- this machine is postgres 10, not postgres 11. same with fatcat-prod1-vm. + +Added to TODO: +- want a better "write lock" flag (on database) other than clearing auth key +- KBART CLOCKSS reports (and maybe LOCKSS?) have repeated lines, need to be merged - empty AUTH_ALT_KEYS should just be ignored (not try to parse) +## Metadata Quality Notes + +- crossref references look great! +- extra/crossref/alternative-id often includes exact full DOI + 10.1158/1538-7445.AM10-3529 + 10.1158/1538-7445.am10-3529 + => but not always? publisher-specific +- contribs[]/extra/seq often has "first" from crossref + => is this helpful? +- abstracts content is fine, but should probably check for "jats:" when setting + mimetype +x BUG: `license_slug` when https://creativecommons.org/licenses/by-nc-sa/4.0 + => https://api.qa.fatcat.wiki/v0/release/55y37c3dtfcw3nw5owugwwhave + 10.26891/jik.v10i2.2016.92-97 +- original title works, yay! + https://api.qa.fatcat.wiki/v0/release/nlmnplhrgbdalcy472hfb2z3im + 10.2504/kds.26.358 +- new license: https://www.karger.com/Services/SiteLicenses +- not copying ISBNs: 10.1016/b978-0-08-037302-7.50022-7 + "9780080373027" + could at least put in alternative-id? +- BUG: subtitle coming through as an array, not string +- `license_slug` does get set + eg for PLOS ONE http://creativecommons.org/licenses/by/4.0/ +- page-one.live.cf.public.springer.com seems to serve up bogus one-pagers; should exclude +- BUG (?): file missing size: + https://fatcat.wiki/file/wpvkiqx2w5celc3ajyfsh3cfsa +- webface BUG: file-to-release links missing +- webface meh: still need to collapse links by domain better, and also vs. www.x/x + +I think this is good (enough)! + +Possible other KBART sources: Hathitrust, PKP preservation net (open, OJS), scholars portal (?), british library + +Nature mag kbart clocks in empty (?) + ISSN-L: 0028-0836 + https://fatcat.wiki/container/drfdii35rzaibj3aml5uhvr5xm + Missing DOIs (out of scope?): DOI not found: 10.1023/a:1009888907797 |